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GEO help: Mouse over screen elements for information. |
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Status |
Public on Nov 30, 2019 |
Title |
Single Cell RNA-seq analysis of gene expression patterns of cells from stem-cell-derived-synthetic-blastocysts, called as 'ES-' or 'EPS-blastoids'. |
Organism |
Mus musculus |
Experiment type |
Expression profiling by high throughput sequencing
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Summary |
To test the efficacy of stem cell lines to generate 'stem-cell-derived-synthetic blastocysts', we dissociated ES- (built by conventional embryonic stem cells and trophoblast stem cells) or EPS-blastoids (built by extended potential pluripotent stem cells and trophoblast stem cells) into single cells following 96h of culture for single-cell transcriptome analysis.
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Overall design |
Examination of gene expression patterns of cells was performed with the single-cell transcriptome analysis following 96h of culture. Single-cell transcriptome analysis was performed using an inDrops v3 barcoding scheme, and the data preprocessing was performed according to the Github inDrops analysis pipeline in order to generate count matrices (https://github.com/indrops/indrops). The transcriptomic analysis comprises three replicates of SB-EP, two replicates of SB-2iLif and one replicate of natural mouse embryo cells at E4.5.
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Contributor(s) |
De Jonghe J, Sozen B, Cox A, Hollfelder F, Zernicka-Goetz M |
Citation(s) |
31846649, 33378662 |
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Submission date |
Jul 13, 2019 |
Last update date |
Feb 22, 2021 |
Contact name |
Florian Hollfelder |
E-mail(s) |
fh111@cam.ac.uk
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Organization name |
University of Cambridge
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Street address |
80 tennis court road
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City |
Cambridge |
ZIP/Postal code |
CB21GA |
Country |
United Kingdom |
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Platforms (1) |
GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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Samples (1) |
GSM3940220 |
SB-EP, SB-2ilif and NatE45 (mixture of 6 samples) |
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Relations |
BioProject |
PRJNA554449 |
SRA |
SRP214529 |
Supplementary file |
Size |
Download |
File type/resource |
GSE134240_RAW.tar |
29.5 Mb |
(http)(custom) |
TAR (of MTX, TSV) |
GSE134240_Readme.txt |
660 b |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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